Loading examples/USER/misc/filter_corotate/in.bpti +1 −1 Original line number Diff line number Diff line Loading @@ -28,7 +28,7 @@ thermo 100 thermo_style multi timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 velocity all create 200.0 12345678 dist uniform #dump dump1 all atom 100 4pti.dump Loading examples/USER/misc/filter_corotate/in.peptide +1 −1 Original line number Diff line number Diff line Loading @@ -20,7 +20,7 @@ thermo 50 timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 fix 1 all nvt temp 250.0 250.0 100.0 tchain 1 fix cor all filter/corotate m 1.0 Loading examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1→examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1 +241 −0 Original line number Diff line number Diff line LAMMPS (10 Mar 2017) LAMMPS (20 Jun 2017) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) using 1 OpenMP thread(s) per MPI task units real Loading Loading @@ -69,13 +70,13 @@ Neighbor list info ... pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory usage (min/avg/max) = 17.8596/1/0 Mbytes Per MPI rank memory allocation (min/avg/max) = 17.86 | 17.86 | 17.86 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3075.6498 943.91164 -2131.7381 -380.67776 241 0 -4503.313 749.58662 -3753.7264 -29.045104 Loop time of 3.35722 on 1 procs for 241 steps with 892 atoms Loop time of 7.63279 on 1 procs for 241 steps with 892 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 32.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Loading @@ -89,14 +90,14 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5003 | 2.5003 | 2.5003 | 0.0 | 74.48 Bond | 0.24287 | 0.24287 | 0.24287 | 0.0 | 7.23 Kspace | 0.53428 | 0.53428 | 0.53428 | 0.0 | 15.91 Neigh | 0.069765 | 0.069765 | 0.069765 | 0.0 | 2.08 Comm | 0.00065374 | 0.00065374 | 0.00065374 | 0.0 | 0.02 Pair | 5.8395 | 5.8395 | 5.8395 | 0.0 | 76.51 Bond | 0.46414 | 0.46414 | 0.46414 | 0.0 | 6.08 Kspace | 1.1535 | 1.1535 | 1.1535 | 0.0 | 15.11 Neigh | 0.14908 | 0.14908 | 0.14908 | 0.0 | 1.95 Comm | 0.001932 | 0.001932 | 0.001932 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009358 | | | 0.28 Other | | 0.02465 | | | 0.32 Nlocal: 892 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -118,10 +119,10 @@ thermo 100 thermo_style multi timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 Respa levels: 1 = bond angle dihedral improper 2 = pair 1 = bond angle 2 = dihedral improper pair 3 = kspace velocity all create 200.0 12345678 dist uniform Loading @@ -145,90 +146,90 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) estimated relative force accuracy = 9.52826e-05 using double precision FFTs 3d grid and FFT values/proc = 9261 4096 Per MPI rank memory usage (min/avg/max) = 19.5425/1/0 Mbytes Per MPI rank memory allocation (min/avg/max) = 19.55 | 19.55 | 19.55 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000 PotEng = -3751.5181 E_bond = 42.2810 E_angle = 345.2592 E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339 E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283 ---------------- Step 100 ----- CPU = 3.9414 (sec) ---------------- TotEng = -2718.8970 KinEng = 538.6206 Temp = 202.8014 PotEng = -3257.5176 E_bond = 203.3367 E_angle = 566.5317 E_dihed = 397.6202 E_impro = 34.6623 E_vdwl = -248.7451 E_coul = -874.5122 E_long = -3336.4111 Press = 135.8662 ---------------- Step 200 ----- CPU = 7.9028 (sec) ---------------- TotEng = -2660.1406 KinEng = 626.3319 Temp = 235.8265 PotEng = -3286.4725 E_bond = 209.5147 E_angle = 591.7773 E_dihed = 388.9591 E_impro = 29.4992 E_vdwl = -243.5808 E_coul = -923.5115 E_long = -3339.1306 Press = 88.9000 ---------------- Step 300 ----- CPU = 11.8246 (sec) ---------------- TotEng = -2673.8090 KinEng = 616.7924 Temp = 232.2346 PotEng = -3290.6014 E_bond = 202.8254 E_angle = 568.6860 E_dihed = 378.4182 E_impro = 38.2399 E_vdwl = -221.3236 E_coul = -915.3004 E_long = -3342.1468 Press = 78.8527 ---------------- Step 400 ----- CPU = 15.7990 (sec) ---------------- TotEng = -2614.9416 KinEng = 649.3474 Temp = 244.4922 PotEng = -3264.2890 E_bond = 211.6116 E_angle = 617.2026 E_dihed = 399.8744 E_impro = 40.2678 E_vdwl = -211.7790 E_coul = -978.1624 E_long = -3343.3041 Press = -4.1958 ---------------- Step 500 ----- CPU = 19.8146 (sec) ---------------- TotEng = -2588.6772 KinEng = 660.1424 Temp = 248.5568 PotEng = -3248.8196 E_bond = 218.4786 E_angle = 620.8605 E_dihed = 390.3220 E_impro = 41.6794 E_vdwl = -226.3657 E_coul = -953.1676 E_long = -3340.6269 Press = 99.3200 ---------------- Step 600 ----- CPU = 23.8587 (sec) ---------------- TotEng = -2550.4618 KinEng = 693.3384 Temp = 261.0557 PotEng = -3243.8002 E_bond = 232.3563 E_angle = 606.2922 E_dihed = 396.2469 E_impro = 37.1980 E_vdwl = -235.8425 E_coul = -937.1208 E_long = -3342.9303 Press = -21.7737 ---------------- Step 700 ----- CPU = 27.8381 (sec) ---------------- TotEng = -2554.4355 KinEng = 692.8951 Temp = 260.8888 PotEng = -3247.3306 E_bond = 216.3395 E_angle = 637.7785 E_dihed = 391.5940 E_impro = 43.1426 E_vdwl = -187.6159 E_coul = -1008.1694 E_long = -3340.3998 Press = 75.1484 ---------------- Step 800 ----- CPU = 31.8039 (sec) ---------------- TotEng = -2508.3551 KinEng = 699.0766 Temp = 263.2163 PotEng = -3207.4317 E_bond = 241.9936 E_angle = 641.3631 E_dihed = 386.2198 E_impro = 43.7793 E_vdwl = -217.7523 E_coul = -964.6070 E_long = -3338.4282 Press = -127.7337 ---------------- Step 900 ----- CPU = 35.7700 (sec) ---------------- TotEng = -2452.7644 KinEng = 762.1842 Temp = 286.9776 PotEng = -3214.9485 E_bond = 243.9191 E_angle = 649.8664 E_dihed = 382.4351 E_impro = 39.0029 E_vdwl = -221.3389 E_coul = -970.8965 E_long = -3337.9366 Press = 122.7720 ---------------- Step 1000 ----- CPU = 39.7695 (sec) ---------------- TotEng = -2386.6805 KinEng = 799.0253 Temp = 300.8490 PotEng = -3185.7058 E_bond = 265.3649 E_angle = 661.7543 E_dihed = 374.6843 E_impro = 38.6877 E_vdwl = -229.2030 E_coul = -960.7041 E_long = -3336.2899 Press = -17.9910 Loop time of 39.7695 on 1 procs for 1000 steps with 892 atoms Performance: 17.380 ns/day, 1.381 hours/ns, 25.145 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads ---------------- Step 100 ----- CPU = 8.4380 (sec) ---------------- TotEng = -2718.4258 KinEng = 539.6265 Temp = 203.1802 PotEng = -3258.0524 E_bond = 203.2307 E_angle = 566.1893 E_dihed = 397.6759 E_impro = 34.7696 E_vdwl = -248.6577 E_coul = -874.8466 E_long = -3336.4135 Press = 135.8640 ---------------- Step 200 ----- CPU = 16.9012 (sec) ---------------- TotEng = -2661.9611 KinEng = 625.0674 Temp = 235.3503 PotEng = -3287.0285 E_bond = 208.1804 E_angle = 590.8462 E_dihed = 389.1482 E_impro = 30.5882 E_vdwl = -240.5448 E_coul = -926.3091 E_long = -3338.9378 Press = 103.4738 ---------------- Step 300 ----- CPU = 25.3046 (sec) ---------------- TotEng = -2662.4139 KinEng = 622.2647 Temp = 234.2951 PotEng = -3284.6785 E_bond = 202.4210 E_angle = 573.6793 E_dihed = 382.8919 E_impro = 41.8973 E_vdwl = -218.9895 E_coul = -924.8414 E_long = -3341.7372 Press = 40.6746 ---------------- Step 400 ----- CPU = 33.8063 (sec) ---------------- TotEng = -2604.9431 KinEng = 662.9890 Temp = 249.6286 PotEng = -3267.9321 E_bond = 195.9116 E_angle = 616.1383 E_dihed = 407.8502 E_impro = 43.3560 E_vdwl = -219.0377 E_coul = -966.3118 E_long = -3345.8387 Press = -91.8856 ---------------- Step 500 ----- CPU = 42.3470 (sec) ---------------- TotEng = -2609.3867 KinEng = 657.0939 Temp = 247.4090 PotEng = -3266.4806 E_bond = 236.4955 E_angle = 570.6256 E_dihed = 390.5111 E_impro = 41.9250 E_vdwl = -223.9927 E_coul = -939.5249 E_long = -3342.5201 Press = 236.7471 ---------------- Step 600 ----- CPU = 50.9590 (sec) ---------------- TotEng = -2564.7161 KinEng = 701.8494 Temp = 264.2603 PotEng = -3266.5655 E_bond = 223.5820 E_angle = 582.7722 E_dihed = 394.6196 E_impro = 43.8581 E_vdwl = -201.7759 E_coul = -967.4136 E_long = -3342.2079 Press = 26.6595 ---------------- Step 700 ----- CPU = 59.4791 (sec) ---------------- TotEng = -2510.1142 KinEng = 689.5931 Temp = 259.6455 PotEng = -3199.7072 E_bond = 254.6476 E_angle = 611.9715 E_dihed = 403.0624 E_impro = 44.1360 E_vdwl = -205.6377 E_coul = -964.7455 E_long = -3343.1416 Press = 60.5789 ---------------- Step 800 ----- CPU = 67.9330 (sec) ---------------- TotEng = -2452.7408 KinEng = 777.5962 Temp = 292.7805 PotEng = -3230.3370 E_bond = 250.4950 E_angle = 656.6738 E_dihed = 382.4702 E_impro = 39.5378 E_vdwl = -225.0375 E_coul = -994.4519 E_long = -3340.0244 Press = -19.6463 ---------------- Step 900 ----- CPU = 76.3690 (sec) ---------------- TotEng = -2339.9766 KinEng = 808.7116 Temp = 304.4961 PotEng = -3148.6883 E_bond = 247.7657 E_angle = 679.0658 E_dihed = 398.2984 E_impro = 43.7890 E_vdwl = -230.2498 E_coul = -945.8152 E_long = -3341.5422 Press = -64.4343 ---------------- Step 1000 ----- CPU = 84.8757 (sec) ---------------- TotEng = -2329.1819 KinEng = 822.9820 Temp = 309.8691 PotEng = -3152.1639 E_bond = 264.9609 E_angle = 691.7104 E_dihed = 385.9914 E_impro = 40.5525 E_vdwl = -230.5182 E_coul = -954.6203 E_long = -3350.2405 Press = -146.6649 Loop time of 84.8758 on 1 procs for 1000 steps with 892 atoms Performance: 8.144 ns/day, 2.947 hours/ns, 11.782 timesteps/s 32.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.169 | 29.169 | 29.169 | 0.0 | 73.34 Bond | 7.6249 | 7.6249 | 7.6249 | 0.0 | 19.17 Kspace | 1.1525 | 1.1525 | 1.1525 | 0.0 | 2.90 Neigh | 0.87606 | 0.87606 | 0.87606 | 0.0 | 2.20 Comm | 0.01563 | 0.01563 | 0.01563 | 0.0 | 0.04 Output | 0.00048423 | 0.00048423 | 0.00048423 | 0.0 | 0.00 Modify | 0.80446 | 0.80446 | 0.80446 | 0.0 | 2.02 Other | | 0.1266 | | | 0.32 Pair | 68.548 | 68.548 | 68.548 | 0.0 | 80.76 Bond | 10.263 | 10.263 | 10.263 | 0.0 | 12.09 Kspace | 2.4528 | 2.4528 | 2.4528 | 0.0 | 2.89 Neigh | 1.9041 | 1.9041 | 1.9041 | 0.0 | 2.24 Comm | 0.044126 | 0.044126 | 0.044126 | 0.0 | 0.05 Output | 0.000983 | 0.000983 | 0.000983 | 0.0 | 0.00 Modify | 1.4113 | 1.4113 | 1.4113 | 0.0 | 1.66 Other | | 0.2516 | | | 0.30 Nlocal: 892 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 27 ave 27 max 27 min Nghost: 38 ave 38 max 38 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146206 ave 146206 max 146206 min Neighs: 144068 ave 144068 max 144068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146206 Ave neighs/atom = 163.908 Total # of neighbors = 144068 Ave neighs/atom = 161.511 Ave special neighs/atom = 10.9395 Neighbor list builds = 186 Neighbor list builds = 190 Dangerous builds = 0 unfix cor Loading @@ -237,4 +238,4 @@ unfix 1 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:43 Total wall time: 0:01:32 examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4→examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4 +241 −0 File changed and moved.Preview size limit exceeded, changes collapsed. Show changes examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1→examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1 +147 −0 Original line number Diff line number Diff line LAMMPS (10 Mar 2017) LAMMPS (20 Jun 2017) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide, run for 8ps in NVT Loading Loading @@ -48,10 +49,10 @@ thermo 50 timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 Respa levels: 1 = bond angle dihedral improper 2 = pair 1 = bond angle 2 = dihedral improper pair 3 = kspace fix 1 all nvt temp 250.0 250.0 100.0 tchain 1 Loading Loading @@ -83,55 +84,55 @@ Neighbor list info ... pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory usage (min/avg/max) = 22.6706/1/0 Mbytes Per MPI rank memory allocation (min/avg/max) = 22.72 | 22.72 | 22.72 Mbytes Step Temp E_pair E_mol TotEng Press 0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821 50 239.46028 -7546.5667 1092.8874 -5023.9668 -24643.891 100 242.81799 -7125.5527 416.0788 -5259.7139 15525.465 150 235.97108 -7531.9334 932.35464 -5190.6987 -14838.489 200 252.06415 -7195.6011 568.02993 -5122.6064 8841.332 250 249.99431 -7586.5092 881.83491 -5212.0676 -9330.345 300 240.3382 -7333.0933 633.29951 -5264.8395 5137.9757 350 255.34529 -7568.2413 856.46371 -5187.2226 -6206.063 400 242.99276 -7419.9031 713.23943 -5255.8602 2447.0091 450 251.10653 -7622.061 844.20584 -5278.6079 -4906.6559 500 255.59314 -7439.253 710.84907 -5202.3691 1571.0032 550 253.2025 -7660.5101 823.05373 -5325.695 -4551.399 600 249.05313 -7509.6729 741.48104 -5281.2046 992.87 650 251.75984 -7593.6589 847.08244 -5243.4286 -3510.1176 700 249.25027 -7601.9112 794.0912 -5319.6557 305.76021 750 255.415 -7602.2674 822.98524 -5254.3109 -2333.421 800 241.99621 -7643.8878 796.53352 -5402.5008 -298.66565 850 253.6428 -7598.3764 816.45457 -5267.5316 -1905.3478 900 247.20231 -7690.2806 789.75999 -5424.5838 -1331.7228 950 255.92583 -7634.7505 831.18272 -5275.5466 -2186.5117 1000 253.2126 -7647.9526 823.93602 -5312.195 -1189.9659 Loop time of 150.664 on 1 procs for 1000 steps with 2004 atoms Performance: 4.588 ns/day, 5.231 hours/ns, 6.637 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984 50 239.47667 -7205.1006 1092.7664 -4682.5237 -23733.122 100 244.63086 -6788.0793 422.97204 -4904.5234 16458.011 150 240.79042 -7267.0791 966.31411 -4863.1107 -13554.894 200 254.77122 -6868.5713 591.00071 -4756.4431 10532.563 250 241.87417 -7264.9349 856.9357 -4963.8743 -9043.4359 300 251.37775 -6976.8 650.55612 -4825.3773 6986.2021 350 250.81494 -7286.7011 880.11184 -4909.0829 -6392.4665 400 247.55673 -7104.4036 701.89555 -4924.4551 4720.7811 450 258.54988 -7215.3011 832.23692 -4839.3759 -3446.3859 500 246.80928 -7151.2468 715.61007 -4962.0464 2637.5769 550 246.20721 -7159.0464 805.24974 -4883.8011 -2725.227 600 250.62483 -7201.7688 806.10076 -4899.2968 770.22352 650 247.59777 -7260.1607 802.97277 -4978.8899 -430.42309 700 246.86951 -7286.2971 825.99865 -4986.3486 -427.88651 750 252.79268 -7307.8572 833.4822 -4965.0605 -614.74372 800 251.73191 -7315.2457 839.59859 -4972.666 952.56448 850 246.75844 -7303.6221 816.67112 -5013.6642 -2055.2823 900 251.00123 -7317.4219 825.12165 -4993.6817 -356.53166 950 259.20822 -7252.3466 854.62611 -4850.1016 -1719.5267 1000 245.72486 -7347.5547 811.48146 -5068.9576 -717.6136 Loop time of 357.523 on 1 procs for 1000 steps with 2004 atoms Performance: 1.933 ns/day, 12.414 hours/ns, 2.797 timesteps/s 32.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 135.81 | 135.81 | 135.81 | 0.0 | 90.14 Bond | 2.5889 | 2.5889 | 2.5889 | 0.0 | 1.72 Kspace | 2.0379 | 2.0379 | 2.0379 | 0.0 | 1.35 Neigh | 5.893 | 5.893 | 5.893 | 0.0 | 3.91 Comm | 1.6998 | 1.6998 | 1.6998 | 0.0 | 1.13 Output | 0.00077915 | 0.00077915 | 0.00077915 | 0.0 | 0.00 Modify | 2 | 2 | 2 | 0.0 | 1.33 Other | | 0.6352 | | | 0.42 Pair | 328.2 | 328.2 | 328.2 | 0.0 | 91.80 Bond | 4.4815 | 4.4815 | 4.4815 | 0.0 | 1.25 Kspace | 3.9448 | 3.9448 | 3.9448 | 0.0 | 1.10 Neigh | 12.457 | 12.457 | 12.457 | 0.0 | 3.48 Comm | 3.2147 | 3.2147 | 3.2147 | 0.0 | 0.90 Output | 0.001689 | 0.001689 | 0.001689 | 0.0 | 0.00 Modify | 3.937 | 3.937 | 3.937 | 0.0 | 1.10 Other | | 1.289 | | | 0.36 Nlocal: 2004 ave 2004 max 2004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11197 ave 11197 max 11197 min Nghost: 11191 ave 11191 max 11191 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 707779 ave 707779 max 707779 min Neighs: 708610 ave 708610 max 708610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 707779 Ave neighs/atom = 353.183 Total # of neighbors = 708610 Ave neighs/atom = 353.598 Ave special neighs/atom = 2.34032 Neighbor list builds = 200 Dangerous builds = 200 Loading @@ -143,4 +144,4 @@ unfix 1 Please see the log.cite file for references relevant to this simulation Total wall time: 0:02:30 Total wall time: 0:05:57 Loading
examples/USER/misc/filter_corotate/in.bpti +1 −1 Original line number Diff line number Diff line Loading @@ -28,7 +28,7 @@ thermo 100 thermo_style multi timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 velocity all create 200.0 12345678 dist uniform #dump dump1 all atom 100 4pti.dump Loading
examples/USER/misc/filter_corotate/in.peptide +1 −1 Original line number Diff line number Diff line Loading @@ -20,7 +20,7 @@ thermo 50 timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 fix 1 all nvt temp 250.0 250.0 100.0 tchain 1 fix cor all filter/corotate m 1.0 Loading
examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1→examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1 +241 −0 Original line number Diff line number Diff line LAMMPS (10 Mar 2017) LAMMPS (20 Jun 2017) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) using 1 OpenMP thread(s) per MPI task units real Loading Loading @@ -69,13 +70,13 @@ Neighbor list info ... pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory usage (min/avg/max) = 17.8596/1/0 Mbytes Per MPI rank memory allocation (min/avg/max) = 17.86 | 17.86 | 17.86 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3075.6498 943.91164 -2131.7381 -380.67776 241 0 -4503.313 749.58662 -3753.7264 -29.045104 Loop time of 3.35722 on 1 procs for 241 steps with 892 atoms Loop time of 7.63279 on 1 procs for 241 steps with 892 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 32.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Loading @@ -89,14 +90,14 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5003 | 2.5003 | 2.5003 | 0.0 | 74.48 Bond | 0.24287 | 0.24287 | 0.24287 | 0.0 | 7.23 Kspace | 0.53428 | 0.53428 | 0.53428 | 0.0 | 15.91 Neigh | 0.069765 | 0.069765 | 0.069765 | 0.0 | 2.08 Comm | 0.00065374 | 0.00065374 | 0.00065374 | 0.0 | 0.02 Pair | 5.8395 | 5.8395 | 5.8395 | 0.0 | 76.51 Bond | 0.46414 | 0.46414 | 0.46414 | 0.0 | 6.08 Kspace | 1.1535 | 1.1535 | 1.1535 | 0.0 | 15.11 Neigh | 0.14908 | 0.14908 | 0.14908 | 0.0 | 1.95 Comm | 0.001932 | 0.001932 | 0.001932 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009358 | | | 0.28 Other | | 0.02465 | | | 0.32 Nlocal: 892 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -118,10 +119,10 @@ thermo 100 thermo_style multi timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 Respa levels: 1 = bond angle dihedral improper 2 = pair 1 = bond angle 2 = dihedral improper pair 3 = kspace velocity all create 200.0 12345678 dist uniform Loading @@ -145,90 +146,90 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) estimated relative force accuracy = 9.52826e-05 using double precision FFTs 3d grid and FFT values/proc = 9261 4096 Per MPI rank memory usage (min/avg/max) = 19.5425/1/0 Mbytes Per MPI rank memory allocation (min/avg/max) = 19.55 | 19.55 | 19.55 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000 PotEng = -3751.5181 E_bond = 42.2810 E_angle = 345.2592 E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339 E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283 ---------------- Step 100 ----- CPU = 3.9414 (sec) ---------------- TotEng = -2718.8970 KinEng = 538.6206 Temp = 202.8014 PotEng = -3257.5176 E_bond = 203.3367 E_angle = 566.5317 E_dihed = 397.6202 E_impro = 34.6623 E_vdwl = -248.7451 E_coul = -874.5122 E_long = -3336.4111 Press = 135.8662 ---------------- Step 200 ----- CPU = 7.9028 (sec) ---------------- TotEng = -2660.1406 KinEng = 626.3319 Temp = 235.8265 PotEng = -3286.4725 E_bond = 209.5147 E_angle = 591.7773 E_dihed = 388.9591 E_impro = 29.4992 E_vdwl = -243.5808 E_coul = -923.5115 E_long = -3339.1306 Press = 88.9000 ---------------- Step 300 ----- CPU = 11.8246 (sec) ---------------- TotEng = -2673.8090 KinEng = 616.7924 Temp = 232.2346 PotEng = -3290.6014 E_bond = 202.8254 E_angle = 568.6860 E_dihed = 378.4182 E_impro = 38.2399 E_vdwl = -221.3236 E_coul = -915.3004 E_long = -3342.1468 Press = 78.8527 ---------------- Step 400 ----- CPU = 15.7990 (sec) ---------------- TotEng = -2614.9416 KinEng = 649.3474 Temp = 244.4922 PotEng = -3264.2890 E_bond = 211.6116 E_angle = 617.2026 E_dihed = 399.8744 E_impro = 40.2678 E_vdwl = -211.7790 E_coul = -978.1624 E_long = -3343.3041 Press = -4.1958 ---------------- Step 500 ----- CPU = 19.8146 (sec) ---------------- TotEng = -2588.6772 KinEng = 660.1424 Temp = 248.5568 PotEng = -3248.8196 E_bond = 218.4786 E_angle = 620.8605 E_dihed = 390.3220 E_impro = 41.6794 E_vdwl = -226.3657 E_coul = -953.1676 E_long = -3340.6269 Press = 99.3200 ---------------- Step 600 ----- CPU = 23.8587 (sec) ---------------- TotEng = -2550.4618 KinEng = 693.3384 Temp = 261.0557 PotEng = -3243.8002 E_bond = 232.3563 E_angle = 606.2922 E_dihed = 396.2469 E_impro = 37.1980 E_vdwl = -235.8425 E_coul = -937.1208 E_long = -3342.9303 Press = -21.7737 ---------------- Step 700 ----- CPU = 27.8381 (sec) ---------------- TotEng = -2554.4355 KinEng = 692.8951 Temp = 260.8888 PotEng = -3247.3306 E_bond = 216.3395 E_angle = 637.7785 E_dihed = 391.5940 E_impro = 43.1426 E_vdwl = -187.6159 E_coul = -1008.1694 E_long = -3340.3998 Press = 75.1484 ---------------- Step 800 ----- CPU = 31.8039 (sec) ---------------- TotEng = -2508.3551 KinEng = 699.0766 Temp = 263.2163 PotEng = -3207.4317 E_bond = 241.9936 E_angle = 641.3631 E_dihed = 386.2198 E_impro = 43.7793 E_vdwl = -217.7523 E_coul = -964.6070 E_long = -3338.4282 Press = -127.7337 ---------------- Step 900 ----- CPU = 35.7700 (sec) ---------------- TotEng = -2452.7644 KinEng = 762.1842 Temp = 286.9776 PotEng = -3214.9485 E_bond = 243.9191 E_angle = 649.8664 E_dihed = 382.4351 E_impro = 39.0029 E_vdwl = -221.3389 E_coul = -970.8965 E_long = -3337.9366 Press = 122.7720 ---------------- Step 1000 ----- CPU = 39.7695 (sec) ---------------- TotEng = -2386.6805 KinEng = 799.0253 Temp = 300.8490 PotEng = -3185.7058 E_bond = 265.3649 E_angle = 661.7543 E_dihed = 374.6843 E_impro = 38.6877 E_vdwl = -229.2030 E_coul = -960.7041 E_long = -3336.2899 Press = -17.9910 Loop time of 39.7695 on 1 procs for 1000 steps with 892 atoms Performance: 17.380 ns/day, 1.381 hours/ns, 25.145 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads ---------------- Step 100 ----- CPU = 8.4380 (sec) ---------------- TotEng = -2718.4258 KinEng = 539.6265 Temp = 203.1802 PotEng = -3258.0524 E_bond = 203.2307 E_angle = 566.1893 E_dihed = 397.6759 E_impro = 34.7696 E_vdwl = -248.6577 E_coul = -874.8466 E_long = -3336.4135 Press = 135.8640 ---------------- Step 200 ----- CPU = 16.9012 (sec) ---------------- TotEng = -2661.9611 KinEng = 625.0674 Temp = 235.3503 PotEng = -3287.0285 E_bond = 208.1804 E_angle = 590.8462 E_dihed = 389.1482 E_impro = 30.5882 E_vdwl = -240.5448 E_coul = -926.3091 E_long = -3338.9378 Press = 103.4738 ---------------- Step 300 ----- CPU = 25.3046 (sec) ---------------- TotEng = -2662.4139 KinEng = 622.2647 Temp = 234.2951 PotEng = -3284.6785 E_bond = 202.4210 E_angle = 573.6793 E_dihed = 382.8919 E_impro = 41.8973 E_vdwl = -218.9895 E_coul = -924.8414 E_long = -3341.7372 Press = 40.6746 ---------------- Step 400 ----- CPU = 33.8063 (sec) ---------------- TotEng = -2604.9431 KinEng = 662.9890 Temp = 249.6286 PotEng = -3267.9321 E_bond = 195.9116 E_angle = 616.1383 E_dihed = 407.8502 E_impro = 43.3560 E_vdwl = -219.0377 E_coul = -966.3118 E_long = -3345.8387 Press = -91.8856 ---------------- Step 500 ----- CPU = 42.3470 (sec) ---------------- TotEng = -2609.3867 KinEng = 657.0939 Temp = 247.4090 PotEng = -3266.4806 E_bond = 236.4955 E_angle = 570.6256 E_dihed = 390.5111 E_impro = 41.9250 E_vdwl = -223.9927 E_coul = -939.5249 E_long = -3342.5201 Press = 236.7471 ---------------- Step 600 ----- CPU = 50.9590 (sec) ---------------- TotEng = -2564.7161 KinEng = 701.8494 Temp = 264.2603 PotEng = -3266.5655 E_bond = 223.5820 E_angle = 582.7722 E_dihed = 394.6196 E_impro = 43.8581 E_vdwl = -201.7759 E_coul = -967.4136 E_long = -3342.2079 Press = 26.6595 ---------------- Step 700 ----- CPU = 59.4791 (sec) ---------------- TotEng = -2510.1142 KinEng = 689.5931 Temp = 259.6455 PotEng = -3199.7072 E_bond = 254.6476 E_angle = 611.9715 E_dihed = 403.0624 E_impro = 44.1360 E_vdwl = -205.6377 E_coul = -964.7455 E_long = -3343.1416 Press = 60.5789 ---------------- Step 800 ----- CPU = 67.9330 (sec) ---------------- TotEng = -2452.7408 KinEng = 777.5962 Temp = 292.7805 PotEng = -3230.3370 E_bond = 250.4950 E_angle = 656.6738 E_dihed = 382.4702 E_impro = 39.5378 E_vdwl = -225.0375 E_coul = -994.4519 E_long = -3340.0244 Press = -19.6463 ---------------- Step 900 ----- CPU = 76.3690 (sec) ---------------- TotEng = -2339.9766 KinEng = 808.7116 Temp = 304.4961 PotEng = -3148.6883 E_bond = 247.7657 E_angle = 679.0658 E_dihed = 398.2984 E_impro = 43.7890 E_vdwl = -230.2498 E_coul = -945.8152 E_long = -3341.5422 Press = -64.4343 ---------------- Step 1000 ----- CPU = 84.8757 (sec) ---------------- TotEng = -2329.1819 KinEng = 822.9820 Temp = 309.8691 PotEng = -3152.1639 E_bond = 264.9609 E_angle = 691.7104 E_dihed = 385.9914 E_impro = 40.5525 E_vdwl = -230.5182 E_coul = -954.6203 E_long = -3350.2405 Press = -146.6649 Loop time of 84.8758 on 1 procs for 1000 steps with 892 atoms Performance: 8.144 ns/day, 2.947 hours/ns, 11.782 timesteps/s 32.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.169 | 29.169 | 29.169 | 0.0 | 73.34 Bond | 7.6249 | 7.6249 | 7.6249 | 0.0 | 19.17 Kspace | 1.1525 | 1.1525 | 1.1525 | 0.0 | 2.90 Neigh | 0.87606 | 0.87606 | 0.87606 | 0.0 | 2.20 Comm | 0.01563 | 0.01563 | 0.01563 | 0.0 | 0.04 Output | 0.00048423 | 0.00048423 | 0.00048423 | 0.0 | 0.00 Modify | 0.80446 | 0.80446 | 0.80446 | 0.0 | 2.02 Other | | 0.1266 | | | 0.32 Pair | 68.548 | 68.548 | 68.548 | 0.0 | 80.76 Bond | 10.263 | 10.263 | 10.263 | 0.0 | 12.09 Kspace | 2.4528 | 2.4528 | 2.4528 | 0.0 | 2.89 Neigh | 1.9041 | 1.9041 | 1.9041 | 0.0 | 2.24 Comm | 0.044126 | 0.044126 | 0.044126 | 0.0 | 0.05 Output | 0.000983 | 0.000983 | 0.000983 | 0.0 | 0.00 Modify | 1.4113 | 1.4113 | 1.4113 | 0.0 | 1.66 Other | | 0.2516 | | | 0.30 Nlocal: 892 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 27 ave 27 max 27 min Nghost: 38 ave 38 max 38 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146206 ave 146206 max 146206 min Neighs: 144068 ave 144068 max 144068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146206 Ave neighs/atom = 163.908 Total # of neighbors = 144068 Ave neighs/atom = 161.511 Ave special neighs/atom = 10.9395 Neighbor list builds = 186 Neighbor list builds = 190 Dangerous builds = 0 unfix cor Loading @@ -237,4 +238,4 @@ unfix 1 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:43 Total wall time: 0:01:32
examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4→examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4 +241 −0 File changed and moved.Preview size limit exceeded, changes collapsed. Show changes
examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1→examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1 +147 −0 Original line number Diff line number Diff line LAMMPS (10 Mar 2017) LAMMPS (20 Jun 2017) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide, run for 8ps in NVT Loading Loading @@ -48,10 +49,10 @@ thermo 50 timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 Respa levels: 1 = bond angle dihedral improper 2 = pair 1 = bond angle 2 = dihedral improper pair 3 = kspace fix 1 all nvt temp 250.0 250.0 100.0 tchain 1 Loading Loading @@ -83,55 +84,55 @@ Neighbor list info ... pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory usage (min/avg/max) = 22.6706/1/0 Mbytes Per MPI rank memory allocation (min/avg/max) = 22.72 | 22.72 | 22.72 Mbytes Step Temp E_pair E_mol TotEng Press 0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821 50 239.46028 -7546.5667 1092.8874 -5023.9668 -24643.891 100 242.81799 -7125.5527 416.0788 -5259.7139 15525.465 150 235.97108 -7531.9334 932.35464 -5190.6987 -14838.489 200 252.06415 -7195.6011 568.02993 -5122.6064 8841.332 250 249.99431 -7586.5092 881.83491 -5212.0676 -9330.345 300 240.3382 -7333.0933 633.29951 -5264.8395 5137.9757 350 255.34529 -7568.2413 856.46371 -5187.2226 -6206.063 400 242.99276 -7419.9031 713.23943 -5255.8602 2447.0091 450 251.10653 -7622.061 844.20584 -5278.6079 -4906.6559 500 255.59314 -7439.253 710.84907 -5202.3691 1571.0032 550 253.2025 -7660.5101 823.05373 -5325.695 -4551.399 600 249.05313 -7509.6729 741.48104 -5281.2046 992.87 650 251.75984 -7593.6589 847.08244 -5243.4286 -3510.1176 700 249.25027 -7601.9112 794.0912 -5319.6557 305.76021 750 255.415 -7602.2674 822.98524 -5254.3109 -2333.421 800 241.99621 -7643.8878 796.53352 -5402.5008 -298.66565 850 253.6428 -7598.3764 816.45457 -5267.5316 -1905.3478 900 247.20231 -7690.2806 789.75999 -5424.5838 -1331.7228 950 255.92583 -7634.7505 831.18272 -5275.5466 -2186.5117 1000 253.2126 -7647.9526 823.93602 -5312.195 -1189.9659 Loop time of 150.664 on 1 procs for 1000 steps with 2004 atoms Performance: 4.588 ns/day, 5.231 hours/ns, 6.637 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984 50 239.47667 -7205.1006 1092.7664 -4682.5237 -23733.122 100 244.63086 -6788.0793 422.97204 -4904.5234 16458.011 150 240.79042 -7267.0791 966.31411 -4863.1107 -13554.894 200 254.77122 -6868.5713 591.00071 -4756.4431 10532.563 250 241.87417 -7264.9349 856.9357 -4963.8743 -9043.4359 300 251.37775 -6976.8 650.55612 -4825.3773 6986.2021 350 250.81494 -7286.7011 880.11184 -4909.0829 -6392.4665 400 247.55673 -7104.4036 701.89555 -4924.4551 4720.7811 450 258.54988 -7215.3011 832.23692 -4839.3759 -3446.3859 500 246.80928 -7151.2468 715.61007 -4962.0464 2637.5769 550 246.20721 -7159.0464 805.24974 -4883.8011 -2725.227 600 250.62483 -7201.7688 806.10076 -4899.2968 770.22352 650 247.59777 -7260.1607 802.97277 -4978.8899 -430.42309 700 246.86951 -7286.2971 825.99865 -4986.3486 -427.88651 750 252.79268 -7307.8572 833.4822 -4965.0605 -614.74372 800 251.73191 -7315.2457 839.59859 -4972.666 952.56448 850 246.75844 -7303.6221 816.67112 -5013.6642 -2055.2823 900 251.00123 -7317.4219 825.12165 -4993.6817 -356.53166 950 259.20822 -7252.3466 854.62611 -4850.1016 -1719.5267 1000 245.72486 -7347.5547 811.48146 -5068.9576 -717.6136 Loop time of 357.523 on 1 procs for 1000 steps with 2004 atoms Performance: 1.933 ns/day, 12.414 hours/ns, 2.797 timesteps/s 32.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 135.81 | 135.81 | 135.81 | 0.0 | 90.14 Bond | 2.5889 | 2.5889 | 2.5889 | 0.0 | 1.72 Kspace | 2.0379 | 2.0379 | 2.0379 | 0.0 | 1.35 Neigh | 5.893 | 5.893 | 5.893 | 0.0 | 3.91 Comm | 1.6998 | 1.6998 | 1.6998 | 0.0 | 1.13 Output | 0.00077915 | 0.00077915 | 0.00077915 | 0.0 | 0.00 Modify | 2 | 2 | 2 | 0.0 | 1.33 Other | | 0.6352 | | | 0.42 Pair | 328.2 | 328.2 | 328.2 | 0.0 | 91.80 Bond | 4.4815 | 4.4815 | 4.4815 | 0.0 | 1.25 Kspace | 3.9448 | 3.9448 | 3.9448 | 0.0 | 1.10 Neigh | 12.457 | 12.457 | 12.457 | 0.0 | 3.48 Comm | 3.2147 | 3.2147 | 3.2147 | 0.0 | 0.90 Output | 0.001689 | 0.001689 | 0.001689 | 0.0 | 0.00 Modify | 3.937 | 3.937 | 3.937 | 0.0 | 1.10 Other | | 1.289 | | | 0.36 Nlocal: 2004 ave 2004 max 2004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11197 ave 11197 max 11197 min Nghost: 11191 ave 11191 max 11191 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 707779 ave 707779 max 707779 min Neighs: 708610 ave 708610 max 708610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 707779 Ave neighs/atom = 353.183 Total # of neighbors = 708610 Ave neighs/atom = 353.598 Ave special neighs/atom = 2.34032 Neighbor list builds = 200 Dangerous builds = 200 Loading @@ -143,4 +144,4 @@ unfix 1 Please see the log.cite file for references relevant to this simulation Total wall time: 0:02:30 Total wall time: 0:05:57
